Virosphere in flux: Old and new viruses in an ancient land

The south-west Australian floristic region is one of 36 United Nations global hotspots of international species diversity. Considering the high biodiversity of the flora, it is likely that the plant virus flora is also abundant and genetically diverse, although only 15 indigenous plant viruses have been described from the flora of Western Australia. Colonisation of Australia by foreign powers from the 1830s onwards saw the introduction of thousands of exotic plant species and their pathogens, including plant viruses. Clearance of the original flora for agriculture and housing has created interfaces between the new exotic flora of exotic crops, pastures, gardens and weeds and the remnants of the original one. The actions of humans and the creation of these interfaces between ecosystems have provided opportunities for exotic viruses to interact with indigenous plants, and for indigenous viruses to interact with exotic hosts. A component of this thesis describes studies to gain a greater understanding of the identity and evolution of the plant viruses present in the indigenous flora of Western Australia and how viruses are adapting to new host opportunities. A metagenomics approach was used to identify virus-like sequences from plant samples along transects that spanned interfaces between highly modified, partially modified and relatively unmodified sites. 78 novel viruses were identified. Most of these were from indigenous plants, and analysis of them confirmed our hypothesis that viruses of this indigenous flora are abundant, genetically diverse and largely unknown. None of the viruses found in indigenous plants also occurred in the exotic plants sampled, or vice versa. The exotic viruses, Catharanthus mosaic virus, barley yellow dwarf virus and white clover mosaic virus, were found in exotic plants at ecosystem interfaces, but not in indigenous plants, suggesting that viral movement across exotic-indigenous floral interfaces may not be widespread. Despite these findings, the continuing invasion by exotic viruses, as evidenced by our discovery in Australia of Catharanthus mosaic virus, demonstrates the failure of quarantine practices to prevent new viruses arriving, thereby posing potential threats to indigenous plants. An indigenous virus might extend its host range to infect exotic weeds or crop plants. We used yellow tailflower mild mottle virus (YTMMV) as a model to test how an indigenous virus might interact with exotic hosts it had never encountered before. YTMMV is a contact-transmissible tobamovirus isolated from endemic Anthocercis species (family Solanaceae). An isolate of YTMMV was passaged through plants of Nicotiana benthamiana, tomato and black nightshade, and its genome was sequenced after every passage to determine the presence of nonsynonymous (NS) and synonymous nucleotide substitutions. Only one fixed NS nucleotide substitution was observed in the intervening region (IR) of the viral genome, and it occurred only in tomato. The passages through tomato were repeated, and a different single NS substitution occurred adjacent to the NS substitution that occurred in the first passage experiment. This finding suggested that NS substitutions in the IR of YTMMV were being selected in tomato. Tobamovirus virions are famously stable under a range of treatments. An assessment of the durability of YTMMV virions under different treatments such as time under different temperature regimes, incubation in milk solution and sodium hydroxide was done. YTMMV was shown to be more resilient to inactivation using these treatments than related viruses, tobacco mosaic virus and green cucumber mild mosaic virus. The study into transmissibility and longevity of virions of YTMMV is a pre-emptive study that will be applicable should YTMMV spill over into crops. The study of plant virus biodiversity in the wild and at the interface of ecosystems will increase our understanding of how viruses influence ecosystems, particularly on resilience to biotic and abiotic stress tolerance, longevity and fecundity. The potential application of such knowledge to agriculture is important, but it is as yet unacknowledged because of the dearth of examples. A far greater research effort is needed to understand the roles viruses play in ecosystems and the molecular mechanisms by which these are achieved. These areas are where in-depth studies of wild plant-virus interactions will have their greatest impact